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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattctgttgctgctttgttcagtactcaaattatcaatatcgtcgatttttcatttggacaaaagatgcagttcttattgaaatcttcaattctgtcagGTAGTAAACATGGAATGGGGCAGTTTCTGGTCATCACATTTGCCAAGAACTCCTTATGACATCTCCCTTGATGATGAGACACAAAACCGCAATGATCAG

Basic information

species Zea mays
transcript GRMZM2G467069_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G467069_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g71320.1 (Oryza sativa), 3'ss of exon 5
gtatattctgttgctgctttgttcagtactcaaattatcaatatcgtcgatttttcatt--------tggacaaaag-----atgcagttcttattgaaatcttcaa---ttctgt----cagGTAGTAAACATGGAATGGGGCAGTTTCTGGTCATCACATTTGCCAAGAACTCCTTATGACATCTCCCTTGATGATGAGACACAAAACCGCAATGATCAG
   |||  | ||    | ||  || ||| |||  | |      | ||| | |  ||||         ||||  ||||     |||  |  | | |    | | | ||   ||  ||    ||||||||||||||||| ||||| | |||||||||||||||||||||||| || || ||||||||||  || |||||||| ||||| || ||||||||||||
--gtatcttattttctcctttatctgtagtcagttcaatttccttgtcaaatgctcatcagcttatgtggagtaaaggaattatgatgcccatgtgcgtaccctaaaacatttcgttaatcagGTAGTAAACATGGAGTGGGGGAATTTCTGGTCATCACATTTGCCAAGGACGCCATATGACATCTTGCTGGATGATGAAACACACAATCGCAATGATCAG

upper sequence: GRMZM2G467069_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv06s0061g00040.t01 (Vitis vinifera), 3'ss of exon 5
-----------gtatattctgttgctgctttgttcagtactcaaattatcaatatcgtcgatttttcatttggacaaaagatgcagttcttattgaaatcttcaattctgtcagGTAGTAAACATGGAATGGGGCAGTTTCTGGTCATCACATTTGCCAAGAACTCCTTATGACATCTCCCTTGATGATGAGACACAAAACCGCAATGATCAG
             || ||||  |  | | ||    |  |||  | || | |  ||      |  ||| | |    |  |  || | ||| | |    |||||| |||| || |||| || |||||||||||||| | |||||||||||||||||||||||||||  |||| || ||     | |||| ||| |  |  || |  |||||||||
gtatcctttcttgattttctagtcatacattacctaacactgcatttttgagaataaagactgattcttctatttattatttg-acttcatgtc---atcttccattc-gttagGTTGTCAACATGGAATGGGGAAATTTCTGGTCATCACATTTGCCAAGAACATCTTACGATATTGATTTAGATGGTGATAGTCCTAATCCAAATGATCAG

upper sequence: GRMZM2G467069_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S414_10V6.1 (Physcomitrella patens), 3'ss of exon 4
gtatattctgttgctgctttgttcagtactcaaattatcaatatcgtcgatttttcatttggacaaaagatgcagttcttattgaaatcttcaattctgtcagGTAGTAAACATGGAATGGGGCAGTTTCTGGTCATCACATTTGCCAAGAACTCCTTATGACATCTCCCTTGATGATGAGACACAAAACCGCAATGATCAG
  |  || | |       ||     |   | | ||| |  |     |  | |  |  | | |    ||   |   | || ||  | |   | |||| || |||||  |||||||||| ||||| | ||||||||||||||||||||| || |||  |   ||    ||| | ||| | ||||     ||||     ||  | 
--acgttgtttcatatgattcccatgagatgatatttttgacgaactaaactagtgctattgttgcaatgcgtcat-ctaatctataggatgaattttgacagGTGATAAACATGGAGTGGGGGAATTTCTGGTCATCACATTTGCCTAGGACTTATGTGGATGAATCCTTGGATAACGAGAGTTTGAACCCAGGAGAATAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 84

GGCTGCTGTGATCATTGGTGCTGGCACCAATGCTTGCTATATTGAACGCACTGATGCAATTATTAAATGTCAGGGTCTTCTTACAAACTCTGGTGGCATGgtatattctg ... attctgtcagGTAGTAAACATGGAATGGGGCAGTTTCTGGTCATCACATTTGCCAAGAACTCCTTATGACATCTCCCTTGATGATGAGACACAAAACCGCAATGATCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 103

GGCTGCTGTGATCATTGGTGCTGGCACCAATGCTTGCTATATTGAACGCACTGATGCAATTATTAAATGTCAGGGTCTTCTTACAAACTCTGGTGGCATGgtatattctg ... attctgtcagGTAGTAAACATGGAATGGGGCAGTTTCTGGTCATCACATTTGCCAAGAACTCCTTATGACATCTCCCTTGATGATGAGACACAAAACCGCAATGATCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 67

GGCTGCTGTGATCATTGGTGCTGGCACCAATGCTTGCTATATTGAACGCACTGATGCAATTATTAAATGTCAGGGTCTTCTTACAAACTCTGGTGGCATGgtatattctg ... attctgtcagGTAGTAAACATGGAATGGGGCAGTTTCTGGTCATCACATTTGCCAAGAACTCCTTATGACATCTCCCTTGATGATGAGACACAAAACCGCAATGATCAG


Block sizes: 46 (upstream exon), 44 (downstream exon)
Score: 65

GGCTGCTGTGATCATTGGTGCTGGCACCAATGCTTGCTATATTGAACGCACTGATGCAATTATTAAATGTCAGGGTCTTCTTACAAACTCTGGTGGCATGgtatattctg ... attctgtcagGTAGTAAACATGGAATGGGGCAGTTTCTGGTCATCACATTTGCCAAGAACTCCTTATGACATCTCCCTTGATGATGAGACACAAAACCGCAATGATCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttttcatttggacaaaagatgcagttcttattgaaatcttcaattctgtcagGTAGTAAACATGGAATGGGGCAGTTTCTGGTCATCACATTTGCCAAGAACTCCTTATGACATCTCCCTTGATGATGAGACACAAAACCGCAATGATCAG
                                              ttctgtc  CT-rich tract
                              ttattgaaat  TA-rich tract